My best of Tom Baker list:

Robot - so-so however it's his debut, that is what makes it worth watching.

Genesis of the Daleks - the Time Lords send the Doctor on a mission to alter Dalek history and make them less violent. Many consider this the first strike of the Time war that happened off screen between the 8th and 9th Doctors.

The Face of Evil - the Doctor meets a new companion and fights an evil computer.

Robots of Death - the plot is ok, but the dialog is quite good.

The Invasion of Time - Great episode, one of the best of the best

The Androids of Tara - One of my all time favorite Doctor Who episodes ever.

City of Death - Douglas Adams, Tom Baker directs, a time traveling chicken, and a JOhn Cleese cameo.

The Creature From the Pit - A really fun episode. Doctor Who faithful will notice the old woman was also the old woman in part two and on of the very first episode starring William Hartnell as The Doctor.

You may also want to check out Legopolis. Tom Baker's final episode.